Examples: pasv-select

You can select sequences by signature using either fixed strings or regular expressions. I will show you examples using both methods.

Note: for a lot more examples of using this and other pasv commands, see here.

Input files

queries.fa

There are 16 queries in the fasta file. Here are the first few sequences.

>Seq_01__AAA__Yes__Yes__Both
AAA
>Seq_02__ABA__Yes__Yes__Both
ABA
>Seq_03__ACB__Yes__Yes__Both
ACB
>Seq_04__ADB__Yes__Yes__Both
ADB
>Seq_05__AAA__Yes__No__Start
AAA

As you can see, it is just some fake data to illustrate the pasv-select program.

signatures.tsv

The signatures file is a tab-separated (TSV) file that looks like this:

name	pos_50	pos_52	pos_54	signature	spans_start	spans_end	spans
Seq_01__AAA__Yes__Yes__Both	A	A	A	AAA	Yes	Yes	Both
Seq_02__ABA__Yes__Yes__Both	A	B	A	ABA	Yes	Yes	Both
Seq_03__ACB__Yes__Yes__Both	A	C	B	ACB	Yes	Yes	Both
Seq_04__ADB__Yes__Yes__Both	A	D	B	ADB	Yes	Yes	Both
Seq_05__AAA__Yes__No__Start	A	A	A	AAA	Yes	No	Start
Seq_06__ABA__Yes__No__Start	A	B	A	ABA	Yes	No	Start
Seq_07__ACB__Yes__No__Start	A	C	B	ACB	Yes	No	Start
Seq_08__ADB__Yes__No__Start	A	D	B	ADB	Yes	No	Start
Seq_09__AAA__No__Yes__End	A	A	A	AAA	No	Yes	End
Seq_10__ABA__No__Yes__End	A	B	A	ABA	No	Yes	End
Seq_11__ACB__No__Yes__End	A	C	B	ACB	No	Yes	End
Seq_12__ADB__No__Yes__End	A	D	B	ADB	No	Yes	End
Seq_13__AAA__No__No__Neither	A	A	A	AAA	No	No	Neither
Seq_14__ABA__No__No__Neither	A	B	A	ABA	No	No	Neither
Seq_15__ACB__No__No__Neither	A	C	B	ACB	No	No	Neither
Seq_16__ADB__No__No__Neither	A	D	B	ADB	No	No	Neither

Set up environment variables

These are some environment variables that we will use in the example scripts. I am assuming you are running this from the following directory with respect to the pasv source directory: ./_examples/pasv_select.

export QUERY_FILE=queries.fa
export SIGNATURE_FILE=signatures.tsv
export OUTDIR=apple

Note that these are just some silly test files...that's why the fasta "sequences" just look like numbers :)

Selecting with fixed strings

Selecting

Select queries with the signature AAA.

# Clean up outdir if it exists.
$ [ -d "${OUTDIR}" ] && rm -r "${OUTDIR}"

# Run pasv-select.
$ pasv select \
    --fixed-strings \
    --outdir="${OUTDIR}" \
    "${QUERY_FILE}" \
    "${SIGNATURE_FILE}" \
    AAA

# Print out the resulting fasta files.
$ for f in $(ls "${OUTDIR}"/*); do echo "=== $f ==="; cat $f; done
=== apple/signature_AAA.fa ===
>Seq_01__AAA__Yes__Yes__Both
AAA
>Seq_05__AAA__Yes__No__Start
AAA
>Seq_09__AAA__No__Yes__End
AAA
>Seq_13__AAA__No__No__Neither
AAA

Rejecting

You can also reject queries with certain signatures by using the --reject flag.

Here is an example of rejecting queries with the signature AAA.

# Clean up outdir if it exists.
$ [ -d "${OUTDIR}" ] && rm -r "${OUTDIR}"

# Run pasv-select.
$ pasv select \
    --reject \
    --fixed-strings \
    --outdir="${OUTDIR}" \
    "${QUERY_FILE}" \
    "${SIGNATURE_FILE}" \
    AAA

# Print out the resulting fasta files.
$ for f in $(ls "${OUTDIR}"/*); do echo "=== $f ==="; cat $f; done
=== apple/signature_ABA.fa ===
>Seq_02__ABA__Yes__Yes__Both
ABA
>Seq_06__ABA__Yes__No__Start
ABA
>Seq_10__ABA__No__Yes__End
ABA
>Seq_14__ABA__No__No__Neither
ABA
=== apple/signature_ACB.fa ===
>Seq_03__ACB__Yes__Yes__Both
ACB
>Seq_07__ACB__Yes__No__Start
ACB
>Seq_11__ACB__No__Yes__End
ACB
>Seq_15__ACB__No__No__Neither
ACB
=== apple/signature_ADB.fa ===
>Seq_04__ADB__Yes__Yes__Both
ADB
>Seq_08__ADB__Yes__No__Start
ADB
>Seq_12__ADB__No__Yes__End
ADB
>Seq_16__ADB__No__No__Neither
ADB

As you see, there are only sequences that have a different signature than AAA.

Multiple patterns

You pass multiple patterns at the same time. If a query has any of the listed signatures it will be printed (or rejected if you pass --reject).

To use multiple signatures, just separate them with commas.

Selecting

# Clean up outdir if it exists.
$ [ -d "${OUTDIR}" ] && rm -r "${OUTDIR}"

# Run pasv-select.
$ pasv select \
    --fixed-strings \
    --outdir="${OUTDIR}" \
    "${QUERY_FILE}" \
    "${SIGNATURE_FILE}" \
    AAA,ABA

# Print out the resulting fasta files.
$ for f in $(ls "${OUTDIR}"/*); do echo "=== $f ==="; cat $f; done
=== apple/signature_AAA.fa ===
>Seq_01__AAA__Yes__Yes__Both
AAA
>Seq_05__AAA__Yes__No__Start
AAA
>Seq_09__AAA__No__Yes__End
AAA
>Seq_13__AAA__No__No__Neither
AAA
=== apple/signature_ABA.fa ===
>Seq_02__ABA__Yes__Yes__Both
ABA
>Seq_06__ABA__Yes__No__Start
ABA
>Seq_10__ABA__No__Yes__End
ABA
>Seq_14__ABA__No__No__Neither
ABA

Rejecting

Rejecting with multiple patterns can be confusing. This example will print sequences that do not have signature AAA or ABA (e.g., ACA, TLA, whatever).

# Clean up outdir if it exists.
$ [ -d "${OUTDIR}" ] && rm -r "${OUTDIR}"n

# Run pasv-select.
$ pasv select \
    --reject \
    --fixed-strings \
    --outdir="${OUTDIR}" \
    "${QUERY_FILE}" \
    "${SIGNATURE_FILE}" \
    AAA,ABA

# Print out the resulting fasta files.
$ for f in $(ls "${OUTDIR}"/*); do echo "=== $f ==="; cat $f; done
=== apple/signature_ACB.fa ===
>Seq_03__ACB__Yes__Yes__Both
ACB
>Seq_07__ACB__Yes__No__Start
ACB
>Seq_11__ACB__No__Yes__End
ACB
>Seq_15__ACB__No__No__Neither
ACB
=== apple/signature_ADB.fa ===
>Seq_04__ADB__Yes__Yes__Both
ADB
>Seq_08__ADB__Yes__No__Start
ADB
>Seq_12__ADB__No__Yes__End
ADB
>Seq_16__ADB__No__No__Neither
ADB

Selecting with regular expressions

You can also use regular expressions to select signatures.

In this file, the sequences only have the following signatures: AAA, ABA, ACB, ADB.

So with this regular expression, [AC].$, I can select any signature with A or C in the 2nd position from the end.

One thing to note, you generally should put the regular expression inside single quotes.

# Clean up outdir if it exists.
$ [ -d "${OUTDIR}" ] && rm -r "${OUTDIR}"

# Run pasv-select.
$ pasv select \
    --outdir="${OUTDIR}" \
    "${QUERY_FILE}" \
    "${SIGNATURE_FILE}" \
    '[AC].$'

# Print out the resulting fasta files.
$ for f in $(ls "${OUTDIR}"/*); do echo "=== $f ==="; cat $f; done
=== apple/signature_AAA.fa ===
>Seq_01__AAA__Yes__Yes__Both
AAA
>Seq_05__AAA__Yes__No__Start
AAA
>Seq_09__AAA__No__Yes__End
AAA
>Seq_13__AAA__No__No__Neither
AAA
=== apple/signature_ACB.fa ===
>Seq_03__ACB__Yes__Yes__Both
ACB
>Seq_07__ACB__Yes__No__Start
ACB
>Seq_11__ACB__No__Yes__End
ACB
>Seq_15__ACB__No__No__Neither
ACB

Note that you can use the --reject flag and with regular expressions, as well as passing in a comma separated list of regular expressions. Just watch out though, it can get a little wonky if you go crazy with the regular expression matching and then try and reject it.